Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Craig, Rory J.; Dueñas, Marco A.; Camacho, Dimitrios J.; Gallaher, Sean D.; Avendaño-Monsalve, Maria Clara; Lin, Yang-Tsung; Blaby-Haas, Crysten E.; Moseley, Jeffrey L.; Merchant, Sabeeha S.

doi:10.1093/plcell/koaf259

Title: Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Journal Article · Mon Oct 27 00:00:00 UTC 2025 · The Plant Cell

DOI: https://doi.org/10.1093/plcell/koaf259 · OSTI ID:3364010

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University of California, Berkeley, CA (United States); University of Melbourne, Parkville, VIC (Australia)
University of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity, and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for the use of Auxenochlorella as a reference organism.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California, Berkeley, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; SC0023027

OSTI ID:: 3364010

Journal Information:: The Plant Cell, Journal Name: The Plant Cell Journal Issue: 11 Vol. 37; ISSN 1532-298X; ISSN 1040-4651

Publisher:: American Society of Plant Biologists (ASPB)Copyright Statement

Country of Publication:: United States

Language:: English

References (197)

Chlorella species as hosts for genetic engineering and expression of heterologous proteins: Progress, challenge and perspective Yang, Bo; Liu, Jin; Jiang, Yue Biotechnology Journal, Vol. 11, Issue 10 https://doi.org/10.1002/biot.201500617	journal	July 2016
Predicting Genes in Single Genomes with AUGUSTUS Hoff, Katharina J.; Stanke, Mario Current Protocols in Bioinformatics, Vol. 65, Issue 1 https://doi.org/10.1002/cpbi.57	journal	November 2018
On the origins and industrial applications of Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids : Origins and applications of S. cerevisiae x S. kudriavzevii hybrids Peris, David; Pérez-Torrado, Roberto; Hittinger, Chris Todd Yeast, Vol. 35, Issue 1 https://doi.org/10.1002/yea.3283	journal	December 2017
The budding yeast life cycle: More complex than anticipated? Fischer, Gilles; Liti, Gianni; Llorente, Bertrand Yeast, Vol. 38, Issue 1 https://doi.org/10.1002/yea.3533	journal	December 2020
Further characterization of the respiratory deficient dum-1 mutation of Chlamydomonas reinhardtii and its use as a recipient for mitochondrial transformation Randolph-Anderson, Barbara L.; Boynton, John E.; Gillham, Nicholas W. Molecular and General Genetics MGG, Vol. 236-236, Issue 2-3 https://doi.org/10.1007/BF00277118	journal	January 1993
Culture conditions affect eicosapentaenoic acid content ofChlorella minutissima Seto, Akira; Wang, H. L.; Hesseltine, C. W. Journal of the American Oil Chemists' Society, Vol. 61, Issue 5 https://doi.org/10.1007/BF02542159	journal	May 1984
Characterization of an ammonium transporter in the oleaginous alga Chlorella protothecoides Yan, Dong; Dai, Junbiao; Wu, Qingyu Applied Microbiology and Biotechnology, Vol. 97, Issue 2 https://doi.org/10.1007/s00253-012-4534-x	journal	November 2012
The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation Garagna, Silvia; Page, Jesus; Fernandez-Donoso, Raul Chromosoma, Vol. 123, Issue 6 https://doi.org/10.1007/s00412-014-0477-6	journal	July 2014
Initial characteristics of RbcX proteins from Arabidopsis thaliana Kolesiński, Piotr; Piechota, Janusz; Szczepaniak, Andrzej Plant Molecular Biology, Vol. 77, Issue 4-5 https://doi.org/10.1007/s11103-011-9823-8	journal	September 2011
Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel `pentapeptide repeat' family of proteins Kieselbach, Thomas; Mant, Alexandra; Robinson, Colin FEBS Letters, Vol. 428, Issue 3 https://doi.org/10.1016/S0014-5793(98)00517-1	journal	May 1998
Characterization of plant carbon substrate utilization by Auxenochlorella protothecoides Vogler, Brian W.; Starkenburg, Shawn R.; Sudasinghe, Nilusha Algal Research, Vol. 34 https://doi.org/10.1016/j.algal.2018.07.001	journal	September 2018
The genus Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies Jagielski, Tomasz; Bakuła, Zofia; Gawor, Jan Algal Research, Vol. 43 https://doi.org/10.1016/j.algal.2019.101639	journal	November 2019
Recent advancements in the genetic engineering of microalgae Sproles, Ashley E.; Fields, Francis J.; Smalley, Tressa N. Algal Research, Vol. 53 https://doi.org/10.1016/j.algal.2020.102158	journal	March 2021
The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and genetic divergence of the haplotypes Biondi, Thomas C.; Kruse, Colin P. S.; Koehler, Samuel I. Algal Research, Vol. 79 https://doi.org/10.1016/j.algal.2024.103431	journal	April 2024
Haematococcus lacustris genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns Marcolungo, Luca; Bellamoli, Francesco; Cecchin, Michela Algal Research, Vol. 80 https://doi.org/10.1016/j.algal.2024.103567	journal	June 2024
From spores to gametes: A sexual life cycle in a symbiotic Trebouxia microalga Gazquez, Ayelén; Bordenave, César Daniel; Montero-Pau, Javier Algal Research, Vol. 84 https://doi.org/10.1016/j.algal.2024.103744	journal	December 2024
Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex Caspy, Ido; Malavath, Tirupathi; Klaiman, Daniel Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1861, Issue 10 https://doi.org/10.1016/j.bbabio.2020.148253	journal	October 2020
Insights into eukaryotic Rubisco assembly — Crystal structures of RbcX chaperones from Arabidopsis thaliana Kolesinski, Piotr; Golik, Przemyslaw; Grudnik, Przemyslaw Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1830, Issue 4 https://doi.org/10.1016/j.bbagen.2012.12.025	journal	April 2013
Structure and Function of RbcX, an Assembly Chaperone for Hexadecameric Rubisco Saschenbrecker, Sandra; Bracher, Andreas; Rao, Karnam Vasudeva Cell, Vol. 129, Issue 6 https://doi.org/10.1016/j.cell.2007.04.025	journal	June 2007
Early Sexual Origins of Homeoprotein Heterodimerization and Evolution of the Plant KNOX/BELL Family Lee, Jae-Hyeok; Lin, Huawen; Joo, Sunjoo Cell, Vol. 133, Issue 5 https://doi.org/10.1016/j.cell.2008.04.028	journal	May 2008
Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes Huff, Jason T.; Zilberman, Daniel Cell, Vol. 156, Issue 6 https://doi.org/10.1016/j.cell.2014.01.029	journal	March 2014
N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas Fu, Ye; Luo, Guan-Zheng; Chen, Kai Cell, Vol. 161, Issue 4 https://doi.org/10.1016/j.cell.2015.04.010	journal	May 2015
The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein Fédry, Juliette; Liu, Yanjie; Péhau-Arnaudet, Gérard Cell, Vol. 168, Issue 5 https://doi.org/10.1016/j.cell.2017.01.024	journal	February 2017
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome Bowman, John L.; Kohchi, Takayuki; Yamato, Katsuyuki T. Cell, Vol. 171, Issue 2 https://doi.org/10.1016/j.cell.2017.09.030	journal	October 2017
Efficient precision editing of endogenous Chlamydomonas reinhardtii genes with CRISPR-Cas Nievergelt, Adrian Pascal; Diener, Dennis Ray; Bogdanova, Aliona Cell Reports Methods, Vol. 3, Issue 8 https://doi.org/10.1016/j.crmeth.2023.100562	journal	August 2023
Pathogenic Allodiploid Hybrids of Aspergillus Fungi Steenwyk, Jacob L.; Lind, Abigail L.; Ries, Laure N. A. Current Biology, Vol. 30, Issue 13 https://doi.org/10.1016/j.cub.2020.04.071	journal	July 2020
Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms Bulankova, Petra; Sekulić, Mirna; Jallet, Denis Current Biology, Vol. 31, Issue 15 https://doi.org/10.1016/j.cub.2021.05.013	journal	August 2021
Development of CRISPR/Cas9 system in Chlorella vulgaris FSP-E to enhance lipid accumulation Lin, Way-Rong; Ng, I-Son Enzyme and Microbial Technology, Vol. 133 https://doi.org/10.1016/j.enzmictec.2019.109458	journal	February 2020
Identification of centromere regions in chromosomes of a unicellular red alga, Cyanidioschyzon merolae Kanesaki, Yu; Imamura, Sousuke; Matsuzaki, Motomichi FEBS Letters, Vol. 589, Issue 11 https://doi.org/10.1016/j.febslet.2015.04.009	journal	April 2015
Isolation and characterization of a novel lutein-producing marine microalga using high throughput screening Asker, Dalal; Awad, Tarek S. Food Research International, Vol. 116 https://doi.org/10.1016/j.foodres.2018.08.093	journal	February 2019
RNA Polymerase II Collision Interrupts Convergent Transcription Hobson, David J.; Wei, Wu; Steinmetz, Lars M. Molecular Cell, Vol. 48, Issue 3 https://doi.org/10.1016/j.molcel.2012.08.027	journal	November 2012
Small cells with big photosynthetic productivities: biotechnological potential of the Picochlorum genus Krishnan, Anagha; Dahlin, Lukas R.; Guarnieri, Michael T. Trends in Biotechnology, Vol. 43, Issue 4 https://doi.org/10.1016/j.tibtech.2024.10.004	journal	April 2025
DNA methylation: a historical perspective Mattei, Alexandra L.; Bailly, Nina; Meissner, Alexander Trends in Genetics, Vol. 38, Issue 7 https://doi.org/10.1016/j.tig.2022.03.010	journal	July 2022
The Chlamydomonas genome project: a decade on Blaby, Ian K.; Blaby-Haas, Crysten E.; Tourasse, Nicolas Trends in Plant Science, Vol. 19, Issue 10 https://doi.org/10.1016/j.tplants.2014.05.008	journal	October 2014
The synthetic future of algal genomes Goold, Hugh D.; Moseley, Jeffrey L.; Lauersen, Kyle J. Cell Genomics, Vol. 4, Issue 3 https://doi.org/10.1016/j.xgen.2024.100505	journal	March 2024
Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii Crozet, Pierre; Navarro, Francisco J.; Willmund, Felix ACS Synthetic Biology, Vol. 7, Issue 9 https://doi.org/10.1021/acssynbio.8b00251	journal	August 2018
Pentapeptide Repeat Proteins ^† Vetting, Matthew W.; Hegde, Subray S.; Fajardo, J. Eduardo Biochemistry, Vol. 45, Issue 1 https://doi.org/10.1021/bi052130w	journal	January 2006
High-resolution mapping of meiotic crossovers and non-crossovers in yeast Mancera, Eugenio; Bourgon, Richard; Brozzi, Alessandro Nature, Vol. 454, Issue 7203 https://doi.org/10.1038/nature07135	journal	July 2008
Coupled chaperone action in folding and assembly of hexadecameric Rubisco Liu, Cuimin; Young, Anna L.; Starling-Windhof, Amanda Nature, Vol. 463, Issue 7278 https://doi.org/10.1038/nature08651	journal	January 2010
Integrative genomics viewer Robinson, James T.; Thorvaldsdóttir, Helga; Winckler, Wendy Nature Biotechnology, Vol. 29, Issue 1 https://doi.org/10.1038/nbt.1754	journal	January 2011
A universal SNP and small-indel variant caller using deep neural networks Poplin, Ryan; Chang, Pi-Chuan; Alexander, David Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4235	journal	September 2018
Non-homologous DNA end joining and alternative pathways to double-strand break repair Chang, Howard H. Y.; Pannunzio, Nicholas R.; Adachi, Noritaka Nature Reviews Molecular Cell Biology, Vol. 18, Issue 8 https://doi.org/10.1038/nrm.2017.48	journal	May 2017
Short- and long-term effects of chromosome mis-segregation and aneuploidy Santaguida, Stefano; Amon, Angelika Nature Reviews Molecular Cell Biology, Vol. 16, Issue 8 https://doi.org/10.1038/nrm4025	journal	July 2015
A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus Lemieux, Claude; Turmel, Monique; Otis, Christian Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12014-x	journal	September 2019
Spontaneous whole-genome duplication restores fertility in interspecific hybrids Charron, Guillaume; Marsit, Souhir; Hénault, Mathieu Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12041-8	journal	September 2019
An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas Neupert, Juliane; Gallaher, Sean D.; Lu, Yinghong Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19983-4	journal	December 2020
How the O2-dependent Mg-protoporphyrin monomethyl ester cyclase forms the fifth ring of chlorophylls Chen, Guangyu E.; Adams, Nathan B. P.; Jackson, Philip J. Nature Plants, Vol. 7, Issue 3 https://doi.org/10.1038/s41477-021-00876-3	journal	March 2021
Interspecific hybridization facilitates niche adaptation in beer yeast Gallone, Brigida; Steensels, Jan; Mertens, Stijn Nature Ecology & Evolution, Vol. 3, Issue 11 https://doi.org/10.1038/s41559-019-0997-9	journal	October 2019
Fermentation innovation through complex hybridization of wild and domesticated yeasts Langdon, Quinn K.; Peris, David; Baker, EmilyClare P. Nature Ecology & Evolution, Vol. 3, Issue 11 https://doi.org/10.1038/s41559-019-0998-8	journal	October 2019
Natural antisense transcripts as versatile regulators of gene expression Werner, Andreas; Kanhere, Aditi; Wahlestedt, Claes Nature Reviews Genetics https://doi.org/10.1038/s41576-024-00723-z	journal	April 2024
Fanzor is a eukaryotic programmable RNA-guided endonuclease Saito, Makoto; Xu, Peiyu; Faure, Guilhem Nature, Vol. 620, Issue 7974 https://doi.org/10.1038/s41586-023-06356-2	journal	June 2023
Haplotype-resolved assembly of diploid genomes without parental data Cheng, Haoyu; Jarvis, Erich D.; Fedrigo, Olivier Nature Biotechnology, Vol. 40, Issue 9 https://doi.org/10.1038/s41587-022-01261-x	journal	March 2022
A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis Li, Xiaobo; Patena, Weronika; Fauser, Friedrich Nature Genetics, Vol. 51, Issue 4 https://doi.org/10.1038/s41588-019-0370-6	journal	March 2019
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms Pardo-Palacios, Francisco J.; Arzalluz-Luque, Angeles; Kondratova, Liudmyla Nature Methods, Vol. 21, Issue 5 https://doi.org/10.1038/s41592-024-02229-2	journal	March 2024
Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca Suzuki, Shigekatsu; Endoh, Rikiya; Manabe, Ri-ichiroh Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-18378-8	journal	January 2018
Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes Severgnini, Marco; Lazzari, Barbara; Capra, Emanuele Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-32992-0	journal	October 2018
Addressing the pervasive scarcity of structural annotation in eukaryotic algae Kwon, Taehyung; Hanschen, Erik R.; Hovde, Blake T. Scientific Reports, Vol. 13, Issue 1 https://doi.org/10.1038/s41598-023-27881-0	journal	January 2023
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology Calhoun, Sara; Bell, Tisza Ann Szeremy; Dahlin, Lukas R. Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-01859-y	journal	March 2021
The dynamics of loss of heterozygosity events in genomes Dutta, Abhishek; Schacherer, Joseph EMBO Reports, Vol. 26, Issue 3 https://doi.org/10.1038/s44319-024-00353-w	journal	January 2025
Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae Yan, Dong; Wang, Yun; Murakami, Tatsuya Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14465	journal	September 2015
Biochemical Taxonomy and Molecular Phylogeny of the Genus Chlorella Sensu lato (Chlorophyta) Huss, Volker A. R.; Frank, Carola; Hartmann, Elke C. Journal of Phycology, Vol. 35, Issue 3 https://doi.org/10.1046/j.1529-8817.1999.3530587.x	journal	June 1999
Systematic genome instability screens in yeast and their potential relevance to cancer Yuen, K. W. Y.; Warren, C. D.; Chen, O. Proceedings of the National Academy of Sciences, Vol. 104, Issue 10 https://doi.org/10.1073/pnas.0610642104	journal	February 2007
Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle Tsai, I. J.; Bensasson, D.; Burt, A. Proceedings of the National Academy of Sciences, Vol. 105, Issue 12 https://doi.org/10.1073/pnas.0707314105	journal	March 2008
Chromosomal duplication is a transient evolutionary solution to stress Yona, A. H.; Manor, Y. S.; Herbst, R. H. Proceedings of the National Academy of Sciences, Vol. 109, Issue 51 https://doi.org/10.1073/pnas.1211150109	journal	November 2012
Transcriptional collision between convergent genes in budding yeast Prescott, E. M.; Proudfoot, N. J. Proceedings of the National Academy of Sciences, Vol. 99, Issue 13 https://doi.org/10.1073/pnas.132270899	journal	June 2002
UV-B photoreceptor-mediated protection of the photosynthetic machinery in Chlamydomonas reinhardtii Allorent, Guillaume; Lefebvre-Legendre, Linnka; Chappuis, Richard Proceedings of the National Academy of Sciences, Vol. 113, Issue 51 https://doi.org/10.1073/pnas.1607695114	journal	December 2016
Diatom centromeres suggest a mechanism for nuclear DNA acquisition Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C. Proceedings of the National Academy of Sciences, Vol. 114, Issue 29 https://doi.org/10.1073/pnas.1700764114	journal	July 2017
Efficient targeted DNA editing and replacement in Chlamydomonas reinhardtii using Cpf1 ribonucleoproteins and single-stranded DNA Ferenczi, Aron; Pyott, Douglas Euan; Xipnitou, Andromachi Proceedings of the National Academy of Sciences, Vol. 114, Issue 51 https://doi.org/10.1073/pnas.1710597114	journal	December 2017
Multiomics resolution of molecular events during a day in the life of Chlamydomonas Strenkert, Daniela; Schmollinger, Stefan; Gallaher, Sean D. Proceedings of the National Academy of Sciences, Vol. 116, Issue 6 https://doi.org/10.1073/pnas.1815238116	journal	January 2019
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Del Cortona, Andrea; Jackson, Christopher J.; Bucchini, François Proceedings of the National Academy of Sciences, Vol. 117, Issue 5 https://doi.org/10.1073/pnas.1910060117	journal	January 2020
RepeatModeler2 for automated genomic discovery of transposable element families Flynn, Jullien M.; Hubley, Robert; Goubert, Clément Proceedings of the National Academy of Sciences, Vol. 117, Issue 17 https://doi.org/10.1073/pnas.1921046117	journal	April 2020
The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic Feng, Lipeng; Mundy, Julia E. A.; Stevenson, Clare E. M. Proceedings of the National Academy of Sciences, Vol. 118, Issue 11 https://doi.org/10.1073/pnas.2016705118	journal	March 2021
Widespread polycistronic gene expression in green algae Gallaher, Sean D.; Craig, Rory J.; Ganesan, Iniyan Proceedings of the National Academy of Sciences, Vol. 118, Issue 7 https://doi.org/10.1073/pnas.2017714118	journal	February 2021
Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells Sui, Yang; Qi, Lei; Wu, Jian-Kun Proceedings of the National Academy of Sciences, Vol. 117, Issue 45 https://doi.org/10.1073/pnas.2018633117	journal	October 2020
Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide Tottey, S.; Block, M. A.; Allen, M. Proceedings of the National Academy of Sciences, Vol. 100, Issue 26 https://doi.org/10.1073/pnas.2136793100	journal	December 2003
Life cycle and functional genomics of the unicellular red alga Galdieria for elucidating algal and plant evolution and industrial use Hirooka, Shunsuke; Itabashi, Takeshi; Ichinose, Takako M. Proceedings of the National Academy of Sciences, Vol. 119, Issue 41 https://doi.org/10.1073/pnas.2210665119	journal	October 2022
Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae Dueñas, Marco A.; Craig, Rory J.; Gallaher, Sean D. Proceedings of the National Academy of Sciences, Vol. 122, Issue 9 https://doi.org/10.1073/pnas.2417695122	journal	February 2025
A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae Liu, Helen W.; Khera, Radhika; Grob, Patricia Proceedings of the National Academy of Sciences, Vol. 122, Issue 25 https://doi.org/10.1073/pnas.2500621122	journal	June 2025
Yeast transformation: a model system for the study of recombination. Orr-Weaver, T. L.; Szostak, J. W.; Rothstein, R. J. Proceedings of the National Academy of Sciences, Vol. 78, Issue 10 https://doi.org/10.1073/pnas.78.10.6354	journal	October 1981
High-frequency nuclear transformation of Chlamydomonas reinhardtii. Kindle, K. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 3 https://doi.org/10.1073/pnas.87.3.1228	journal	February 1990
Purification and Characterization of a Novel Phosphorus-oxidizing Enzyme from Pseudomonas stutzeri WM88 Costas, Amaya M. Garcia; White, Andrea K.; Metcalf, William W. Journal of Biological Chemistry, Vol. 276, Issue 20 https://doi.org/10.1074/jbc.M011764200	journal	February 2001
Proteome Map of the Chloroplast Lumen of Arabidopsis thaliana Schubert, Maria; Petersson, Ulrika A.; Haas, Brian J. Journal of Biological Chemistry, Vol. 277, Issue 10 https://doi.org/10.1074/jbc.M108575200	journal	November 2001
The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage Karpowicz, Steven J.; Prochnik, Simon E.; Grossman, Arthur R. Journal of Biological Chemistry, Vol. 286, Issue 24 https://doi.org/10.1074/jbc.M111.233734	journal	April 2011
Conserved Chloroplast Open-reading Frame ycf54 Is Required for Activity of the Magnesium Protoporphyrin Monomethylester Oxidative Cyclase in Synechocystis PCC 6803 Hollingshead, Sarah; Kopečná, Jana; Jackson, Philip J. Journal of Biological Chemistry, Vol. 287, Issue 33 https://doi.org/10.1074/jbc.M112.352526	journal	June 2012
An Engineered Streptomyces hygroscopicus aph 7″ Gene Mediates Dominant Resistance against Hygromycin B in Chlamydomonas reinhardtii Berthold, Peter; Schmitt, Rüdiger; Mages, Wolfgang Protist, Vol. 153, Issue 4 https://doi.org/10.1078/14344610260450136	journal	December 2002
Stable nuclear transformation of Chlamydomonas using the Chlamydomonas gene for nitrate reductase Kindle, K. L. The Journal of Cell Biology, Vol. 109, Issue 6 https://doi.org/10.1083/jcb.109.6.2589	journal	December 1989
FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia Lin, Jianfeng; Le, Thuc Vy; Augspurger, Katherine Molecular Biology of the Cell, Vol. 30, Issue 21 https://doi.org/10.1091/mbc.E19-07-0367	journal	October 2019
New strategies to improve minimap2 alignment accuracy Li, Heng Bioinformatics, Vol. 37, Issue 23 https://doi.org/10.1093/bioinformatics/btab705	journal	October 2021
Using native and syntenically mapped cDNA alignments to improve de novo gene finding Stanke, Mario; Diekhans, Mark; Baertsch, Robert Bioinformatics, Vol. 24, Issue 5 https://doi.org/10.1093/bioinformatics/btn013	journal	January 2008
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
BEDTools: a flexible suite of utilities for comparing genomic features Quinlan, Aaron R.; Hall, Ira M. Bioinformatics, Vol. 26, Issue 6 https://doi.org/10.1093/bioinformatics/btq033	journal	January 2010
STAR: ultrafast universal RNA-seq aligner Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts635	journal	October 2012
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1. Hoff, Katharina J.; Lange, Simone; Lomsadze, Alexandre Bioinformatics, Vol. 32, Issue 5 https://doi.org/10.1093/bioinformatics/btv661	journal	November 2015
Hybridization and the origin of new yeast lineages Gabaldón, Toni FEMS Yeast Research, Vol. 20, Issue 5 https://doi.org/10.1093/femsyr/foaa040	journal	July 2020
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage Benites, Luis Felipe; Bucchini, François; Sanchez-Brosseau, Sophie Genome Biology and Evolution, Vol. 13, Issue 10 https://doi.org/10.1093/gbe/evab216	journal	October 2021
A High Frequency of Chromosomal Duplications in Unicellular Algae Is Compensated by Translational Regulation Krasovec, Marc; Merret, Rémy; Sanchez, Frédéric Genome Biology and Evolution, Vol. 15, Issue 6 https://doi.org/10.1093/gbe/evad086	journal	May 2023
Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales Fulnečková, Jana; Hasíková, Tereza; Fajkus, Jiří Genome Biology and Evolution, Vol. 4, Issue 3 https://doi.org/10.1093/gbe/evs007	journal	January 2012
High-Efficiency Transformation of Chlamydomonas reinhardtii by Electroporation Shimogawara, Kosuke; Fujiwara, Shoko; Grossman, Arthur Genetics, Vol. 148, Issue 4 https://doi.org/10.1093/genetics/148.4.1821	journal	April 1998
Twelve years of SAMtools and BCFtools Danecek, Petr; Bonfield, James K.; Liddle, Jennifer GigaScience, Vol. 10, Issue 2 https://doi.org/10.1093/gigascience/giab008	journal	January 2021
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era Minh, Bui Quang; Schmidt, Heiko A.; Chernomor, Olga Molecular Biology and Evolution, Vol. 37, Issue 5 https://doi.org/10.1093/molbev/msaa015	journal	February 2020
MEGA11: Molecular Evolutionary Genetics Analysis Version 11 Tamura, Koichiro; Stecher, Glen; Kumar, Sudhir Molecular Biology and Evolution, Vol. 38, Issue 7 https://doi.org/10.1093/molbev/msab120	journal	April 2021
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes Manni, Mosè; Berkeley, Matthew R.; Seppey, Mathieu Molecular Biology and Evolution, Vol. 38, Issue 10 https://doi.org/10.1093/molbev/msab199	journal	July 2021
The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants Petroll, Romy; Papareddy, Ranjith K.; Krela, Rafal Molecular Biology and Evolution, Vol. 42, Issue 4 https://doi.org/10.1093/molbev/msaf064	journal	March 2025
Permuted tRNA Genes in the Nuclear and Nucleomorph Genomes of Photosynthetic Eukaryotes Maruyama, S.; Sugahara, J.; Kanai, A. Molecular Biology and Evolution, Vol. 27, Issue 5 https://doi.org/10.1093/molbev/msp313	journal	December 2009
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
Loss of Heterozygosity Drives Adaptation in Hybrid Yeast Smukowski Heil, Caiti S.; DeSevo, Christopher G.; Pai, Dave A. Molecular Biology and Evolution, Vol. 34, Issue 7 https://doi.org/10.1093/molbev/msx098	journal	March 2017
Genomic Analysis of Picochlorum Species Reveals How Microalgae May Adapt to Variable Environments Foflonker, Fatima; Mollegard, Devin; Ong, Meichin Molecular Biology and Evolution https://doi.org/10.1093/molbev/msy167	journal	September 2018
Mitochondrial genes in the colourless algaPrototheca wickerhamiiresemble plant genes in their exons but fungal genes in their introns Wolf, Gabriele; Burger, Gertraud; Lang, B. Franz Nucleic Acids Research, Vol. 21, Issue 3 https://doi.org/10.1093/nar/21.3.719	journal	January 1993
Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii Chaux-Jukic, Frédéric; O’Donnell, Samuel; Craig, Rory J. Nucleic Acids Research, Vol. 49, Issue 13 https://doi.org/10.1093/nar/gkab534	journal	June 2021
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes Chan, Patricia P.; Lin, Brian Y.; Mak, Allysia J. Nucleic Acids Research, Vol. 49, Issue 16 https://doi.org/10.1093/nar/gkab688	journal	August 2021
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes Yoon, Peter H.; Skopintsev, Petr; Shi, Honglue Nucleic Acids Research, Vol. 51, Issue 22 https://doi.org/10.1093/nar/gkad1053	journal	November 2023
Biochemical characterisation of Mer3 helicase interactions and the protection of meiotic recombination intermediates Altmannova, Veronika; Firlej, Magdalena; Müller, Franziska Nucleic Acids Research, Vol. 51, Issue 9 https://doi.org/10.1093/nar/gkad175	journal	March 2023
Transcriptional regulation of human DNA repair genes following genotoxic stress: trigger mechanisms, inducible responses and genotoxic adaptation Christmann, M.; Kaina, B. Nucleic Acids Research, Vol. 41, Issue 18 https://doi.org/10.1093/nar/gkt635	journal	July 2013
Identification of protein coding regions in RNA transcripts Tang, Shiyuyun; Lomsadze, Alexandre; Borodovsky, Mark Nucleic Acids Research, Vol. 43, Issue 12 https://doi.org/10.1093/nar/gkv227	journal	April 2015
GeSeq – versatile and accurate annotation of organelle genomes Tillich, Michael; Lehwark, Pascal; Pellizzer, Tommaso Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx391	journal	May 2017
Nutritional Control of cell Pigmentation in Chlorella Protothecoides with Special Reference to the Degeneration of Chloroplast Induced by Glucose1 Shihira-Ishikawa, Ikuko; Hase, Eiji Plant and Cell Physiology, Vol. 5, Issue 2 https://doi.org/10.1093/oxfordjournals.pcp.a079037	journal	May 1964
Changes in Contents of Carbohydrate and Fatty acid in the Cells of Chlorella Protothecoides During the Processes of de- and Re-Generation of Chloroplasts Matsuka, Mitsuo; Otsuka, Hama; Hase, Eiji Plant and Cell Physiology, Vol. 7, Issue 4 https://doi.org/10.1093/oxfordjournals.pcp.a079217	journal	December 1966
Improvement of Culture Conditions and Evidence for Nuclear Transformation by Homologous Recombination in a Red Alga, Cyanidioschyzon merolae 10D Minoda, Ayumi; Sakagami, Rei; Yagisawa, Fumi Plant and Cell Physiology, Vol. 45, Issue 6 https://doi.org/10.1093/pcp/pch087	journal	June 2004
Comparative genomics of Chlamydomonas Craig, Rory J.; Hasan, Ahmed R.; Ness, Rob W. The Plant Cell, Vol. 33, Issue 4 https://doi.org/10.1093/plcell/koab026	journal	February 2021
The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory Craig, Rory J.; Gallaher, Sean D.; Shu, Shengqiang The Plant Cell, Vol. 35, Issue 2 https://doi.org/10.1093/plcell/koac347	journal	December 2022
Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas Akella, Soujanya; Ma, Xinrong; Bacova, Romana Plant Physiology, Vol. 187, Issue 4 https://doi.org/10.1093/plphys/kiab418	journal	September 2021
Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis da Roza, Patrick A.; Muller, Héloïse; Sullivan, Geraldine J. Microbial Genomics, Vol. 10, Issue 4 https://doi.org/10.1099/mgen.0.001223	journal	April 2024
Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates Ning, Jue; Otto, Thomas D.; Pfander, Claudia Genes & Development, Vol. 27, Issue 10 https://doi.org/10.1101/gad.212746.112	journal	May 2013
Genetic and phenotypic intra-species variation in Candida albicans Hirakawa, Matthew P.; Martinez, Diego A.; Sakthikumar, Sharadha Genome Research, Vol. 25, Issue 3 https://doi.org/10.1101/gr.174623.114	journal	December 2014
Fitness benefits of loss of heterozygosity in Saccharomyces hybrids Lancaster, Samuel M.; Payen, Celia; Smukowski Heil, Caiti Genome Research, Vol. 29, Issue 10 https://doi.org/10.1101/gr.245605.118	journal	September 2019
Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii López-Cortegano, Eugenio; Craig, Rory J.; Chebib, Jobran Genome Research, Vol. 33, Issue 1 https://doi.org/10.1101/gr.276957.122	journal	December 2022
Subcellular Localization of the Inducible Chlorella HUP1 Monosaccharide-H+ Symporter and Cloning of a Co-Induced Galactose-H+ Symporter Stadler, R.; Wolf, K.; Hilgarth, C. Plant Physiology, Vol. 107, Issue 1 https://doi.org/10.1104/pp.107.1.33	journal	January 1995
Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle Lopez, David Adrian; Hamaji, Takashi; Kropat, Janette Plant Physiology https://doi.org/10.1104/pp.15.00861	journal	October 2015
Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii Joo, Sunjoo; Nishimura, Yoshiki; Cronmiller, Evan Plant Physiology, Vol. 175, Issue 1 https://doi.org/10.1104/pp.17.00731	journal	July 2017
The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex Blanc, Guillaume; Duncan, Garry; Agarkova, Irina The Plant Cell, Vol. 22, Issue 9 https://doi.org/10.1105/tpc.110.076406	journal	September 2010
LAP6/POLYKETIDE SYNTHASE A and LAP5/POLYKETIDE SYNTHASE B Encode Hydroxyalkyl α-Pyrone Synthases Required for Pollen Development and Sporopollenin Biosynthesis in Arabidopsis thaliana Kim, Sung Soo; Grienenberger, Etienne; Lallemand, Benjamin The Plant Cell, Vol. 22, Issue 12 https://doi.org/10.1105/tpc.110.080028	journal	December 2010
An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii Li, Xiaobo; Zhang, Ru; Patena, Weronika The Plant Cell, Vol. 28, Issue 2 https://doi.org/10.1105/tpc.15.00465	journal	January 2016
A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism Salomé, Patrice A.; Merchant, Sabeeha S. The Plant Cell, Vol. 31, Issue 8 https://doi.org/10.1105/tpc.18.00952	journal	June 2019
Structure of the RuBisCO chaperone RbcX fromSynechocystissp. PCC6803 Tanaka, Shiho; Sawaya, Michael R.; Kerfeld, Cheryl A. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 10 https://doi.org/10.1107/S090744490704228X	journal	September 2007
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii: A revised mineral nutrient supplement for Chlamydomonas Kropat, Janette; Hong-Hermesdorf, Anne; Casero, David The Plant Journal, Vol. 66, Issue 5 https://doi.org/10.1111/j.1365-313X.2011.04537.x	journal	March 2011
MOLECULAR PHYLOGENY AND PHENOTYPIC VARIATION IN THE HETEROTROPHIC GREEN ALGAL GENUS PROTOTHECA (TREBOUXIOPHYCEAE, CHLOROPHYTA)¹ Ueno, Ryohei; Hanagata, Nobutaka; Urano, Naoto Journal of Phycology, Vol. 41, Issue 6 https://doi.org/10.1111/j.1529-8817.2005.00142.x	journal	November 2005
Interspecies hybridization and recombination in Saccharomyces wine yeasts Sipiczki, Matthias FEMS Yeast Research, Vol. 8, Issue 7 https://doi.org/10.1111/j.1567-1364.2008.00369.x	journal	November 2008
Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? Torres-Machorro, Ana Lilia; Hernández, Roberto; Cevallos, Ana María FEMS Microbiology Reviews, Vol. 34, Issue 1 https://doi.org/10.1111/j.1574-6976.2009.00196.x	journal	January 2010
Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae, Chlorophyta) Darienko, Tatyana; Pröschold, Thomas Journal of Phycology, Vol. 51, Issue 2 https://doi.org/10.1111/jpy.12279	journal	March 2015
Meiotic genes and sexual reproduction in the green algal class Trebouxiophyceae (Chlorophyta) Fučíková, Karolina; Pažoutová, Marie; Rindi, Fabio Journal of Phycology, Vol. 51, Issue 3 https://doi.org/10.1111/jpy.12293	journal	April 2015
Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. “desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata, supported by a high‐quality genome assembly Sanders, Claire K.; Hanschen, Erik R.; Biondi, Thomas C. Journal of Phycology, Vol. 58, Issue 3 https://doi.org/10.1111/jpy.13242	journal	March 2022
When the lights go out: the evolutionary fate of free‐living colorless green algae Figueroa‐Martinez, Francisco; Nedelcu, Aurora M.; Smith, David R. New Phytologist, Vol. 206, Issue 3 https://doi.org/10.1111/nph.13279	journal	January 2015
Transcriptional gene fusions via targeted integration at safe harbors for high transgene expression in Chlamydomonas reinhardtii Jacobebbinghaus, Nick; Bigge, Florian; Saudhof, Merve New Phytologist, Vol. 247, Issue 6 https://doi.org/10.1111/nph.70368	journal	July 2025
A novel genetic engineering platform for the effective management of biological contaminants for the production of microalgae Loera-Quezada, Maribel M.; Leyva-González, Marco Antonio; Velázquez-Juárez, Gilberto Plant Biotechnology Journal, Vol. 14, Issue 10 https://doi.org/10.1111/pbi.12564	journal	May 2016
Efficient gene targeting and removal of foreign DNA by homologous recombination in the picoeukaryote Ostreococcus Lozano, Jean-Claude; Schatt, Philippe; Botebol, Hugo The Plant Journal, Vol. 78, Issue 6 https://doi.org/10.1111/tpj.12530	journal	May 2014
Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga Arriola, Matthew B.; Velmurugan, Natarajan; Zhang, Ying The Plant Journal, Vol. 93, Issue 3 https://doi.org/10.1111/tpj.13789	journal	January 2018
A giant type I polyketide synthase participates in zygospore maturation in Chlamydomonas reinhardtii Heimerl, Natalie; Hommel, Elisabeth; Westermann, Martin The Plant Journal, Vol. 95, Issue 2 https://doi.org/10.1111/tpj.13948	journal	June 2018
Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions Cecchin, Michela; Marcolungo, Luca; Rossato, Marzia The Plant Journal, Vol. 100, Issue 6 https://doi.org/10.1111/tpj.14508	journal	September 2019
The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle Strenkert, Daniela; Yildirim, Asli; Yan, Juying The Plant Journal, Vol. 112, Issue 2 https://doi.org/10.1111/tpj.15948	journal	September 2022
Plant PAXX has an XLF ‐like function and stimulates DNA end joining by the Ku‐DNA ligase IV/XRCC4 complex Khan, Hira; Ochi, Takashi The Plant Journal, Vol. 116, Issue 1 https://doi.org/10.1111/tpj.16359	journal	June 2023
Synthetic minichromosomes in plants: past, present, and promise Birchler, James A.; Kelly, Jacob; Singh, Jasnoor The Plant Journal, Vol. 120, Issue 6 https://doi.org/10.1111/tpj.17142	journal	November 2024
Genome editing in the green alga Chlamydomonas: past, present practice and future prospects Nievergelt, Adrian P. The Plant Journal, Vol. 122, Issue 1 https://doi.org/10.1111/tpj.70140	journal	April 2025
Aneuploidy and Isochromosome Formation in Drug-Resistant Candida albicans Selmecki, A. Science, Vol. 313, Issue 5785 https://doi.org/10.1126/science.1128242	journal	July 2006
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions Merchant, S. S.; Prochnik, S. E.; Vallon, O. Science, Vol. 318, Issue 5848, p. 245-250 https://doi.org/10.1126/science.1143609	journal	October 2007
Permuted tRNA Genes Expressed via a Circular RNA Intermediate in Cyanidioschyzon merolae Soma, A.; Onodera, A.; Sugahara, J. Science, Vol. 318, Issue 5849 https://doi.org/10.1126/science.1145718	journal	October 2007
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation Zemach, A.; McDaniel, I. E.; Silva, P. Science, Vol. 328, Issue 5980 https://doi.org/10.1126/science.1186366	journal	April 2010
Chloroplast transformation in Chlamydomonas with high velocity microprojectiles Boynton, J.; Gillham, N.; Harris, E. Science, Vol. 240, Issue 4858 https://doi.org/10.1126/science.2897716	journal	June 1988
FEA1 , FEA2 , and FRE1 , Encoding Two Homologous Secreted Proteins and a Candidate Ferrireductase, Are Expressed Coordinately with FOX1 and FTR1 in Iron-Deficient Chlamydomonas reinhardtii Allen, Michael D.; del Campo, José A.; Kropat, Janette Eukaryotic Cell, Vol. 6, Issue 10 https://doi.org/10.1128/EC.00205-07	journal	July 2007
Phased Diploid Genome Sequence for the Fast-Growing Microalga Picochlorum celeri Becker, Scott A.; Spreafico, Roberto; Kit, Jennie L. Microbiology Resource Announcements, Vol. 9, Issue 20 https://doi.org/10.1128/MRA.00087-20	journal	May 2020
Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum Dale, Angela L.; Feau, Nicolas; Everhart, Sydney E. mBio, Vol. 10, Issue 2 https://doi.org/10.1128/mBio.02452-18	journal	April 2019
Nutritional basis for relating Prototheca and Chlorella Pore, R. Scott Canadian Journal of Microbiology, Vol. 18, Issue 7 https://doi.org/10.1139/m72-183	journal	July 1972
Comparative and Functional Algal Genomics Blaby-Haas, Crysten E.; Merchant, Sabeeha S. Annual Review of Plant Biology, Vol. 70, Issue 1 https://doi.org/10.1146/annurev-arplant-050718-095841	journal	April 2019
The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress Vande Zande, Pétra; Zhou, Xin; Selmecki, Anna Annual Review of Microbiology, Vol. 77, Issue 1 https://doi.org/10.1146/annurev-micro-041320-112443	journal	September 2023
The Role of Hybridization in Plant Speciation Soltis, Pamela S.; Soltis, Douglas E. Annual Review of Plant Biology, Vol. 60, Issue 1 https://doi.org/10.1146/annurev.arplant.043008.092039	journal	June 2009
C HLAMYDOMONAS AS A M ODEL O RGANISM Harris, Elizabeth H. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 52, Issue 1 https://doi.org/10.1146/annurev.arplant.52.1.363	journal	June 2001
Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes Gao, Chunfang; Wang, Yun; Shen, Yue BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-582	journal	January 2014
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements Bao, Weidong; Jurka, Jerzy Mobile DNA, Vol. 4, Issue 1 https://doi.org/10.1186/1759-8753-4-12	journal	January 2013
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane Genome Biology, Vol. 13, Issue 5 https://doi.org/10.1186/gb-2012-13-5-r39	journal	January 2012
A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis Bakuła, Zofia; Siedlecki, Paweł; Gromadka, Robert BMC Genomics, Vol. 22, Issue 1 https://doi.org/10.1186/s12864-021-07491-8	journal	March 2021
Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae Wang, Bo; Jia, Yanyan; Dang, Ningxin BMC Genomics, Vol. 25, Issue 1 https://doi.org/10.1186/s12864-024-10280-8	journal	April 2024
Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida Joo, Sunjoo; Wang, Ming Hsiu; Lui, Gary BMC Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12915-018-0605-5	journal	November 2018
Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution Barten, Robin; van Workum, Dirk-Jan M.; de Bakker, Emma BMC Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s12915-022-01431-y	journal	October 2022
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions Trincado, Juan L.; Entizne, Juan C.; Hysenaj, Gerald Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1417-1	journal	March 2018
OrthoFinder: phylogenetic orthology inference for comparative genomics Emms, David M.; Kelly, Steven Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1832-y	journal	November 2019
A beginner’s guide to manual curation of transposable elements Goubert, Clement; Craig, Rory J.; Bilat, Agustin F. Mobile DNA, Vol. 13, Issue 1 https://doi.org/10.1186/s13100-021-00259-7	journal	March 2022
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage Marcet-Houben, Marina; Gabaldón, Toni PLOS Biology, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pbio.1002220	journal	August 2015
A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium Pombert, Jean-François; Blouin, Nicolas Achille; Lane, Chris PLoS Genetics, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pgen.1004355	journal	May 2014
The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis Pryszcz, Leszek P.; Németh, Tibor; Saus, Ester PLOS Genetics, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pgen.1005626	journal	October 2015
Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species Schröder, Markus S.; Martinez de San Vicente, Kontxi; Prandini, Tâmara H. R. PLOS Genetics, Vol. 12, Issue 11 https://doi.org/10.1371/journal.pgen.1006404	journal	November 2016
Gene Targeting in the Red Alga Cyanidioschyzon merolae: Single- and Multi-Copy Insertion Using Authentic and Chimeric Selection Markers Fujiwara, Takayuki; Ohnuma, Mio; Yoshida, Masaki PLoS ONE, Vol. 8, Issue 9 https://doi.org/10.1371/journal.pone.0073608	journal	September 2013
SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes Drillon, Guénola; Carbone, Alessandra; Fischer, Gilles PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0092621	journal	March 2014
Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii Bracher, Andreas; Hauser, Thomas; Liu, Cuimin PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0135448	journal	August 2015
Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms Moore, Eric R.; Bullington, Briana S.; Weisberg, Alexandra J. PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0181098	journal	July 2017
Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames Cross, Frederick R. G3: Genes\|Genomes\|Genetics, Vol. 6, Issue 2 https://doi.org/10.1534/g3.115.023119	journal	December 2015
A Genetic Screen for Increased Loss of Heterozygosity in Saccharomyces cerevisiae Andersen, Marguerite P.; Nelson, Zara W.; Hetrick, Elizabeth D. Genetics, Vol. 179, Issue 3 https://doi.org/10.1534/genetics.108.089250	journal	June 2008
Detecting sequence signals in targeting peptides using deep learning Almagro Armenteros, Jose Juan; Salvatore, Marco; Emanuelsson, Olof Life Science Alliance, Vol. 2, Issue 5 https://doi.org/10.26508/lsa.201900429	journal	September 2019
Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution Guo, Jian; Jian, Jianbo; Wang, Lili Frontiers in Cellular and Infection Microbiology, Vol. 12 https://doi.org/10.3389/fcimb.2022.797017	journal	February 2022
A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine Pontes, Ana; Čadež, Neža; Gonçalves, Paula Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00449	journal	May 2019
Identification of Sporopollenin as the Outer Layer of Cell Wall in Microalga Chlorella protothecoides He, Xi; Dai, Junbiao; Wu, Qingyu Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01047	journal	June 2016
Molecular Advancements Establishing Chlamydomonas as a Host for Biotechnological Exploitation Schroda, Michael; Remacle, Claire Frontiers in Plant Science, Vol. 13 https://doi.org/10.3389/fpls.2022.911483	journal	June 2022
Good News for Nuclear Transgene Expression in Chlamydomonas Schroda, Michael Cells, Vol. 8, Issue 12 https://doi.org/10.3390/cells8121534	journal	November 2019
Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer Park, Sang-Hyuck; Kyndt, John A.; Brown, Judith K. Life, Vol. 12, Issue 3 https://doi.org/10.3390/life12030458	journal	March 2022
Growth and Cell Size of Microalga Auxenochlorella protothecoides AS-1 under Different Trophic Modes Chen, Haoyu; Sosa, Ana; Chen, Feng Microorganisms, Vol. 12, Issue 4 https://doi.org/10.3390/microorganisms12040835	journal	April 2024
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM Li, Heng arXiv https://doi.org/10.48550/arXiv.1303.3997	preprint	January 2013
From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature Sasso, Severin; Stibor, Herwig; Mittag, Maria eLife, Vol. 7 https://doi.org/10.7554/eLife.39233	journal	November 2018
Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants Hisanaga, Tetsuya; Fujimoto, Shota; Cui, Yihui eLife, Vol. 10 https://doi.org/10.7554/eLife.57090	journal	September 2021
Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds Dutta, Abhishek; Dutreux, Fabien; Schacherer, Joseph eLife, Vol. 10 https://doi.org/10.7554/eLife.70339	journal	June 2021

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